ChAMP

DOI: 10.18129/B9.bioc.ChAMP    

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

Bioconductor version: Release (3.13)

The package includes quality control metrics, a selection of normalization methods and novel methods to identify differentially methylated regions and to highlight copy number alterations.

Author: Yuan Tian [cre,aut], Tiffany Morris [ctb], Lee Stirling [ctb], Andrew Feber [ctb], Andrew Teschendorff [ctb], Ankur Chakravarthy [ctb]

Maintainer: Yuan Tian <champ450k at gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ChAMP")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ChAMP")

 

HTML	R Script	ChAMP: The Chip Analysis Methylation Pipeline
PDF		Reference Manual
Text		NEWS

Details

biocViews	CopyNumber, DNAMethylation, MethylationArray, Microarray, Normalization, Software, TwoChannel
Version	2.22.0
In Bioconductor since	BioC 2.13 (R-3.0) (8 years)
License	GPL-3
Depends	R (>= 3.3), minfi, ChAMPdata(>= 2.6.0), DMRcate, Illumina450ProbeVariants.db, IlluminaHumanMethylationEPICmanifest, DT, RPMM
Imports	prettydoc, Hmisc, globaltest, sva, illuminaio, rmarkdown, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, limma, DNAcopy, preprocessCore, impute, marray, wateRmelon, plyr, goseq, missMethyl, kpmt, ggplot2, GenomicRanges, qvalue, isva, doParallel, bumphunter, quadprog, shiny, shinythemes, plotly (>= 4.5.6), RColorBrewer, dendextend, matrixStats, combinat
LinkingTo
Suggests	knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me	GeoTcgaData
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	ChAMP_2.22.0.tar.gz
Windows Binary	ChAMP_2.22.0.zip
macOS 10.13 (High Sierra)	ChAMP_2.22.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ChAMP
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ChAMP
Package Short Url	https://bioconductor.org/packages/ChAMP/
Package Downloads Report	Download Stats